HEADER LIGASE 12-FEB-20 6VT6 TITLE NAEGLERIA GRUBERI RNA LIGASE K170A MUTANT WITH ATP AND MN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAEGLERIA GRUBERI; SOURCE 3 ORGANISM_COMMON: AMOEBA; SOURCE 4 ORGANISM_TAXID: 5762; SOURCE 5 GENE: NAEGRDRAFT_82186; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA REPAIR, ADENYLYLTRANSFERASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.C.UNCIULEAC,Y.GOLDGUR,S.SHUMAN REVDAT 4 11-OCT-23 6VT6 1 LINK REVDAT 3 10-JUN-20 6VT6 1 JRNL REVDAT 2 06-MAY-20 6VT6 1 JRNL REVDAT 1 08-APR-20 6VT6 0 JRNL AUTH M.C.UNCIULEAC,Y.GOLDGUR,S.SHUMAN JRNL TITL CAVEAT MUTATOR: ALANINE SUBSTITUTIONS FOR CONSERVED AMINO JRNL TITL 2 ACIDS IN RNA LIGASE ELICIT UNEXPECTED REARRANGEMENTS OF THE JRNL TITL 3 ACTIVE SITE FOR LYSINE ADENYLYLATION. JRNL REF NUCLEIC ACIDS RES. V. 48 5603 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32315072 JRNL DOI 10.1093/NAR/GKAA238 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 47215 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.320 REMARK 3 FREE R VALUE TEST SET COUNT : 3895 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.5700 - 5.9760 0.98 1583 119 0.1642 0.2141 REMARK 3 2 5.9760 - 4.7447 0.98 1562 141 0.1440 0.1644 REMARK 3 3 4.7447 - 4.1453 0.99 1551 140 0.1222 0.1642 REMARK 3 4 4.1453 - 3.7665 1.00 1604 152 0.1374 0.1766 REMARK 3 5 3.7665 - 3.4966 0.97 1557 139 0.1396 0.2173 REMARK 3 6 3.4966 - 3.2905 0.99 1560 139 0.1401 0.1709 REMARK 3 7 3.2905 - 3.1258 0.99 1594 139 0.1504 0.2135 REMARK 3 8 3.1258 - 2.9897 0.99 1580 146 0.1630 0.2307 REMARK 3 9 2.9897 - 2.8746 0.99 1544 152 0.1610 0.2250 REMARK 3 10 2.8746 - 2.7755 0.96 1511 149 0.1676 0.2014 REMARK 3 11 2.7755 - 2.6887 0.98 1548 151 0.1720 0.2382 REMARK 3 12 2.6887 - 2.6118 0.99 1571 142 0.1713 0.1917 REMARK 3 13 2.6118 - 2.5431 0.99 1586 159 0.1640 0.2459 REMARK 3 14 2.5431 - 2.4810 0.98 1554 151 0.1776 0.2612 REMARK 3 15 2.4810 - 2.4246 0.99 1540 124 0.1674 0.2409 REMARK 3 16 2.4246 - 2.3730 0.99 1592 148 0.1739 0.2269 REMARK 3 17 2.3730 - 2.3256 0.99 1583 140 0.1725 0.2233 REMARK 3 18 2.3256 - 2.2817 0.97 1517 130 0.1765 0.2515 REMARK 3 19 2.2817 - 2.2409 0.97 1608 132 0.1874 0.2469 REMARK 3 20 2.2409 - 2.2030 0.98 1491 140 0.1895 0.2407 REMARK 3 21 2.2030 - 2.1674 0.98 1593 153 0.1954 0.2914 REMARK 3 22 2.1674 - 2.1341 0.98 1549 134 0.2013 0.2454 REMARK 3 23 2.1341 - 2.1027 0.97 1522 138 0.2011 0.2682 REMARK 3 24 2.1027 - 2.0731 0.98 1646 141 0.2128 0.2642 REMARK 3 25 2.0731 - 2.0451 0.96 1489 132 0.2093 0.2906 REMARK 3 26 2.0451 - 2.0185 0.95 1500 135 0.2221 0.2650 REMARK 3 27 2.0185 - 1.9933 0.93 1511 152 0.2342 0.3266 REMARK 3 28 1.9933 - 1.9692 0.82 1239 112 0.2778 0.3307 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 58 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.6576 -17.8510 -17.0473 REMARK 3 T TENSOR REMARK 3 T11: 0.2438 T22: 0.2277 REMARK 3 T33: 0.2223 T12: 0.0449 REMARK 3 T13: 0.0101 T23: 0.0275 REMARK 3 L TENSOR REMARK 3 L11: 0.2381 L22: 0.4364 REMARK 3 L33: 0.1684 L12: -0.0601 REMARK 3 L13: 0.0585 L23: -0.2979 REMARK 3 S TENSOR REMARK 3 S11: 0.1247 S12: 0.2596 S13: 0.0588 REMARK 3 S21: 0.0183 S22: -0.1469 S23: -0.1371 REMARK 3 S31: -0.0469 S32: 0.0933 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 59 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.5649 -8.7829 -14.9867 REMARK 3 T TENSOR REMARK 3 T11: 0.2389 T22: 0.2179 REMARK 3 T33: 0.3258 T12: 0.0349 REMARK 3 T13: -0.0119 T23: 0.0834 REMARK 3 L TENSOR REMARK 3 L11: 0.3130 L22: 0.8828 REMARK 3 L33: 0.2157 L12: -0.0572 REMARK 3 L13: -0.2289 L23: -0.1833 REMARK 3 S TENSOR REMARK 3 S11: 0.0700 S12: 0.1180 S13: 0.2354 REMARK 3 S21: 0.0844 S22: -0.2868 S23: -0.5872 REMARK 3 S31: -0.0262 S32: 0.1209 S33: -0.0037 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 138 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.8653 8.8874 -6.3943 REMARK 3 T TENSOR REMARK 3 T11: 0.3592 T22: 0.2434 REMARK 3 T33: 0.2854 T12: -0.0178 REMARK 3 T13: -0.0354 T23: 0.0312 REMARK 3 L TENSOR REMARK 3 L11: 0.0498 L22: 0.0559 REMARK 3 L33: 0.1124 L12: 0.0041 REMARK 3 L13: 0.0068 L23: 0.1290 REMARK 3 S TENSOR REMARK 3 S11: 0.1855 S12: -0.0181 S13: 0.1480 REMARK 3 S21: -0.1840 S22: -0.1447 S23: -0.0762 REMARK 3 S31: -0.0348 S32: -0.2011 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 139 THROUGH 340 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.7605 -0.9436 -4.4539 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.1815 REMARK 3 T33: 0.1811 T12: 0.0064 REMARK 3 T13: 0.0101 T23: -0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.4561 L22: 0.9376 REMARK 3 L33: 1.2521 L12: -0.2331 REMARK 3 L13: -0.1949 L23: 0.5689 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: -0.0423 S13: -0.0286 REMARK 3 S21: -0.0353 S22: -0.0756 S23: 0.0978 REMARK 3 S31: 0.0434 S32: -0.1087 S33: -0.0001 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6VT6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000247040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47215 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.39500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5COT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NGRNLK170A (9.8 MG/ML) WAS ADJUSTED TO REMARK 280 5 MM AMP AND 2 MM MNCL2 AND INCUBATED FOR 15 MIN ON ICE BEFORE REMARK 280 ALIQUOTS OF THE PROTEIN SOLUTION (1 UL) WERE MIXED ON A REMARK 280 COVERSLIP WITH AN EQUAL VOLUME OF PRECIPITANT SOLUTION REMARK 280 CONTAINING 0.1 M HEPES PH 6.5, 30% PEG6000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.76467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.88233 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 1 REMARK 465 MET A 2 REMARK 465 GLY A 3 REMARK 465 VAL A 4 REMARK 465 ARG A 5 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 122 O2G ATP A 401 1.31 REMARK 500 O HOH A 657 O HOH A 714 2.03 REMARK 500 O HOH A 610 O HOH A 688 2.11 REMARK 500 O3B ATP A 401 O HOH A 501 2.18 REMARK 500 O HOH A 518 O HOH A 677 2.18 REMARK 500 O HOH A 749 O HOH A 750 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 536 O HOH A 708 2564 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 35 CB CYS A 35 SG -0.101 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 31 -128.33 53.00 REMARK 500 ASP A 54 -9.16 85.87 REMARK 500 ASP A 60 92.62 -165.11 REMARK 500 THR A 129 -73.84 -34.32 REMARK 500 THR A 146 43.22 -92.17 REMARK 500 ASP A 183 -121.42 56.55 REMARK 500 ASN A 291 54.73 -157.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 786 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 787 DISTANCE = 7.23 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 54 OD2 REMARK 620 2 ATP A 401 O1G 115.1 REMARK 620 3 HOH A 552 O 165.3 67.6 REMARK 620 4 HOH A 601 O 88.0 72.2 79.0 REMARK 620 5 HOH A 692 O 86.0 144.9 85.2 81.5 REMARK 620 6 HOH A 729 O 93.4 117.4 97.9 168.2 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 147 OD1 REMARK 620 2 ATP A 401 O3G 158.0 REMARK 620 3 ATP A 401 O1A 77.2 101.4 REMARK 620 4 HOH A 501 O 70.6 87.8 94.1 REMARK 620 5 HOH A 507 O 94.2 107.3 80.9 164.7 REMARK 620 6 HOH A 516 O 80.8 98.1 157.8 76.1 103.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 512 O REMARK 620 2 HOH A 561 O 93.9 REMARK 620 3 HOH A 587 O 88.4 89.7 REMARK 620 4 HOH A 640 O 87.6 85.1 173.2 REMARK 620 5 HOH A 646 O 87.4 171.3 98.9 86.3 REMARK 620 6 HOH A 684 O 170.2 95.9 91.7 93.2 82.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 404 DBREF 6VT6 A 2 340 UNP D2W2Z5 D2W2Z5_NAEGR 1 339 SEQADV 6VT6 SER A 1 UNP D2W2Z5 EXPRESSION TAG SEQADV 6VT6 ALA A 171 UNP D2W2Z5 LYS 170 ENGINEERED MUTATION SEQRES 1 A 340 SER MET GLY VAL ARG LYS LEU ALA THR ILE ARG THR ALA SEQRES 2 A 340 GLY GLU ILE THR PRO ILE ALA GLY ALA GLU ALA ILE GLU SEQRES 3 A 340 CYS CYS HIS VAL ASP GLY TRP THR CYS VAL ILE LYS LYS SEQRES 4 A 340 GLY GLU PHE LYS GLN GLY ASP ARG GLY VAL TYR PHE GLU SEQRES 5 A 340 ILE ASP SER PHE ILE LYS GLU ASP ASN ASP ARG TYR PRO SEQRES 6 A 340 MET LEU SER LYS GLN VAL ILE ASP TYR GLU GLY GLN ARG SEQRES 7 A 340 GLY THR ARG LEU ARG THR ALA ARG LEU ARG GLY GLN LEU SEQRES 8 A 340 SER GLN GLY LEU PHE LEU PRO MET ASP ARG PHE PRO GLU SEQRES 9 A 340 LEU ALA SER ASN GLN VAL GLY ASP ASP VAL THR GLU ILE SEQRES 10 A 340 LEU GLY ILE THR LYS TRP GLU PRO PRO ILE SER THR ASN SEQRES 11 A 340 LEU SER GLY GLU ILE LEU GLY GLU PHE PRO THR PHE ILE SEQRES 12 A 340 SER LYS THR ASP GLN GLU ARG VAL GLN ASN LEU ILE PRO SEQRES 13 A 340 GLN ILE GLU GLU ASN LYS GLY GLN LYS PHE GLU VAL THR SEQRES 14 A 340 VAL ALA LEU ASP GLY SER SER MET THR VAL TYR ARG LYS SEQRES 15 A 340 ASP ASP HIS ILE GLY VAL CYS GLY ARG ASN TRP GLU LEU SEQRES 16 A 340 ARG GLU THR ALA THR ASN ALA GLN TRP HIS ALA ALA ARG SEQRES 17 A 340 ARG ASN LYS MET ILE GLU GLY LEU GLN PHE LEU ASN ARG SEQRES 18 A 340 ASN LEU ALA LEU GLN GLY GLU ILE ILE GLY GLU SER ILE SEQRES 19 A 340 GLN GLY ASN LEU GLU LYS LEU LYS GLY GLN ASP PHE TYR SEQRES 20 A 340 LEU PHE ASP ILE TYR ASP ILE ASP LYS ALA GLN TYR LEU SEQRES 21 A 340 THR PRO ILE GLU ARG GLN SER LEU VAL LYS GLN LEU ASN SEQRES 22 A 340 ASP ASN GLY PHE THR VAL LYS HIS VAL PRO ILE LEU ASP SEQRES 23 A 340 ASP LEU GLU LEU ASN HIS THR ALA GLU GLN ILE LEU ALA SEQRES 24 A 340 MET ALA ASP GLY PRO SER LEU ASN LYS ASN VAL LYS ARG SEQRES 25 A 340 GLU GLY LEU VAL PHE LYS ARG LEU ASP GLY LYS PHE SER SEQRES 26 A 340 PHE LYS ALA ILE SER ASN ALA TYR LEU GLU LYS HIS LYS SEQRES 27 A 340 ASP ARG HET ATP A 401 31 HET MN A 402 1 HET MN A 403 1 HET MN A 404 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 MN 3(MN 2+) FORMUL 6 HOH *287(H2 O) HELIX 1 AA1 TYR A 64 VAL A 71 5 8 HELIX 2 AA2 ASP A 100 ALA A 106 5 7 HELIX 3 AA3 SER A 128 SER A 132 5 5 HELIX 4 AA4 ARG A 150 ASN A 153 5 4 HELIX 5 AA5 LEU A 154 ASN A 161 1 8 HELIX 6 AA6 ASN A 201 ASN A 210 1 10 HELIX 7 AA7 LYS A 211 ASN A 220 1 10 HELIX 8 AA8 THR A 261 ASN A 275 1 15 HELIX 9 AA9 THR A 293 ASP A 302 1 10 HELIX 10 AB1 SER A 330 HIS A 337 1 8 SHEET 1 AA1 3 ALA A 8 THR A 12 0 SHEET 2 AA1 3 ARG A 47 PHE A 51 -1 O TYR A 50 N THR A 9 SHEET 3 AA1 3 LEU A 95 PRO A 98 -1 O LEU A 95 N PHE A 51 SHEET 1 AA2 3 ILE A 16 PRO A 18 0 SHEET 2 AA2 3 ILE A 25 VAL A 30 -1 O CYS A 27 N THR A 17 SHEET 3 AA2 3 TRP A 33 LYS A 38 -1 O CYS A 35 N CYS A 28 SHEET 1 AA3 4 ILE A 72 TYR A 74 0 SHEET 2 AA3 4 GLN A 77 ARG A 81 -1 O GLN A 77 N TYR A 74 SHEET 3 AA3 4 SER A 55 LYS A 58 -1 N ILE A 57 O THR A 80 SHEET 4 AA3 4 THR A 121 LYS A 122 -1 O THR A 121 N PHE A 56 SHEET 1 AA4 2 ALA A 85 LEU A 87 0 SHEET 2 AA4 2 GLN A 90 SER A 92 -1 O SER A 92 N ALA A 85 SHEET 1 AA5 7 ILE A 135 GLU A 138 0 SHEET 2 AA5 7 TRP A 193 LEU A 195 -1 O GLU A 194 N LEU A 136 SHEET 3 AA5 7 HIS A 185 CYS A 189 -1 N VAL A 188 O LEU A 195 SHEET 4 AA5 7 SER A 175 LYS A 182 -1 N THR A 178 O CYS A 189 SHEET 5 AA5 7 LEU A 223 GLY A 231 -1 O LEU A 225 N VAL A 179 SHEET 6 AA5 7 GLN A 244 ASP A 253 -1 O ASP A 250 N GLN A 226 SHEET 7 AA5 7 GLN A 258 TYR A 259 -1 O GLN A 258 N ASP A 253 SHEET 1 AA6 7 ILE A 135 GLU A 138 0 SHEET 2 AA6 7 TRP A 193 LEU A 195 -1 O GLU A 194 N LEU A 136 SHEET 3 AA6 7 HIS A 185 CYS A 189 -1 N VAL A 188 O LEU A 195 SHEET 4 AA6 7 SER A 175 LYS A 182 -1 N THR A 178 O CYS A 189 SHEET 5 AA6 7 LEU A 223 GLY A 231 -1 O LEU A 225 N VAL A 179 SHEET 6 AA6 7 GLN A 244 ASP A 253 -1 O ASP A 250 N GLN A 226 SHEET 7 AA6 7 LYS A 280 HIS A 281 1 O LYS A 280 N LEU A 248 SHEET 1 AA7 4 LEU A 288 GLU A 289 0 SHEET 2 AA7 4 LYS A 165 ALA A 171 -1 N PHE A 166 O LEU A 288 SHEET 3 AA7 4 GLY A 314 ARG A 319 -1 O LYS A 318 N GLU A 167 SHEET 4 AA7 4 SER A 325 ILE A 329 -1 O PHE A 326 N PHE A 317 LINK OD2 ASP A 54 MN MN A 402 1555 1555 2.52 LINK OD1 ASP A 147 MN MN A 404 1555 1555 2.23 LINK O1G ATP A 401 MN MN A 402 1555 1555 2.11 LINK O3G ATP A 401 MN MN A 404 1555 1555 2.63 LINK O1A ATP A 401 MN MN A 404 1555 1555 2.17 LINK MN MN A 402 O HOH A 552 1555 1555 2.58 LINK MN MN A 402 O HOH A 601 1555 1555 2.53 LINK MN MN A 402 O HOH A 692 1555 1555 2.29 LINK MN MN A 402 O HOH A 729 1555 1555 2.19 LINK MN MN A 403 O HOH A 512 1555 1555 2.37 LINK MN MN A 403 O HOH A 561 1555 1555 2.26 LINK MN MN A 403 O HOH A 587 1555 1555 2.14 LINK MN MN A 403 O HOH A 640 1555 1555 1.81 LINK MN MN A 403 O HOH A 646 1555 1555 2.35 LINK MN MN A 403 O HOH A 684 1555 1555 2.16 LINK MN MN A 404 O HOH A 501 1555 1555 2.38 LINK MN MN A 404 O HOH A 507 1555 1555 2.30 LINK MN MN A 404 O HOH A 516 1555 1555 2.46 SITE 1 AC1 29 LYS A 122 THR A 146 ASP A 147 GLN A 148 SITE 2 AC1 29 THR A 169 VAL A 170 ALA A 171 LEU A 172 SITE 3 AC1 29 SER A 176 ARG A 191 GLU A 228 PHE A 249 SITE 4 AC1 29 VAL A 282 VAL A 316 LYS A 318 LYS A 327 SITE 5 AC1 29 MN A 402 MN A 404 HOH A 501 HOH A 507 SITE 6 AC1 29 HOH A 512 HOH A 531 HOH A 548 HOH A 552 SITE 7 AC1 29 HOH A 561 HOH A 580 HOH A 601 HOH A 640 SITE 8 AC1 29 HOH A 651 SITE 1 AC2 6 ASP A 54 ATP A 401 HOH A 552 HOH A 601 SITE 2 AC2 6 HOH A 692 HOH A 729 SITE 1 AC3 6 HOH A 512 HOH A 561 HOH A 587 HOH A 640 SITE 2 AC3 6 HOH A 646 HOH A 684 SITE 1 AC4 5 ASP A 147 ATP A 401 HOH A 501 HOH A 507 SITE 2 AC4 5 HOH A 516 CRYST1 54.935 54.935 101.647 90.00 90.00 120.00 P 32 3 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018203 0.010510 0.000000 0.00000 SCALE2 0.000000 0.021019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009838 0.00000